AIMC Topic: Computational Biology

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Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins.

NAR genomics and bioinformatics
We have evaluated the prediction accuracy of three different tools, deep-learning-based AlphaFold2, AlphaFold3, and large language model-based ESMFold, utilizing the experimentally derived structures deposited in the Protein Data Bank between 2022 an...

Identification of cell senescence-related genes in spontaneous preterm birth based on bioinformatics analysis and machine learning.

PloS one
Spontaneous premature birth (SPTB) is a common pregnancy complication; however, few studies have explored cell senescence-related markers in SPTB. Bioinformatics and machine learning approaches were used to predict potential biomarkers associated wit...

Genetic relationships between the gut microbiota and prostate cancer: Mendelian randomization combined with bioinformatics analysis.

The aging male : the official journal of the International Society for the Study of the Aging Male
BACKGROUND: Prostate cancer (PCa) is a leading cause of male cancer-related death globally. While the gut microbiota is linked to PCa, its genetic association remains unclear.

Food-borne bacterial pathogens: emerging approaches in detection and prevention.

Archives of microbiology
Food-borne bacterial pathogens remain a major public health concern, causing extensive illness and economic losses worldwide. Conventional detection methods are often slow and insufficient for identifying viable but non-culturable pathogens. Recent m...

Targeting CXCL8 in post-traumatic stress disorder and Alzheimer's disease: insights from cross-disorder molecular analysis.

Annals of medicine
BACKGROUND: Emerging clinical evidence indicates that post-traumatic stress disorder (PTSD) may accelerate Alzheimer's disease progression, yet the molecular mechanisms linking these disorders remain poorly understood.

IFNg_DeepKG: A Novel Model for Identifying Interferon-Gamma-Inducing Epitopes Using Knowledge Graph RAG in Biomedical Applications.

Journal of chemical information and modeling
The accurate and efficient computational identification of interferon-gamma-inducing epitopes (IFNgIE) is a critical bottleneck in the design of next-generation vaccines and immunotherapies. Existing computational models, while adept at learning sequ...

Similarity-guided swarm of models: enhancing semi-supervised learning in computational pathology.

Scientific reports
High-precision pixel-level annotation has been a major bottleneck in computational pathology due to its time-consuming nature and reliance on expert knowledge. Semi-supervised learning (SSL) provides a promising approach to alleviate this challenge b...

Identification of PANoptosis-associated genes in hepatic ischemia-reperfusion injury by integrated bioinformatics analysis and machine learning.

PloS one
BACKGROUND: In the context of liver resection and transplantation, hepatic ischemia-reperfusion injury (hepatic IRI) remains a significant clinical challenge, profoundly impacting both postoperative short- and long-term recovery. A novel cell death p...

Identification of coagulation-related hub genes in ischemic stroke based on bioinformatics integration analysis and investigation of their immune regulatory mechanisms.

European journal of medical research
BACKGROUND: Ischemic stroke (IS) is a cerebrovascular disease resulting from insufficient blood supply to specific areas of the brain, often due to atherosclerosis and thrombosis. While the association between polymorphisms in coagulation-related gen...

Unraveling tissue-specific molecular targets of dihydroartemisinin in non-small cell lung cancer: an integrative machine learning and network pharmacology approach.

Medical oncology (Northwood, London, England)
Non-small cell lung cancer (NSCLC) presents significant therapeutic challenges due to resistance and immune evasion. Dihydroartemisinin (DHA), a derivative of artemisinin, exhibits broad anti-tumor activity, but its molecular targets and mechanisms i...